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Inferring single-cell copy number profiles through cross-cell segmentation of read counts
BackgroundCopy number alteration (CNA) is one of the major genomic variations that frequently occur in cancers, and accurate inference of CNAs is...
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Completing a genomic characterisation of microscopic tumour samples with copy number
BackgroundGenomic insights in settings where tumour sample sizes are limited to just hundreds or even tens of cells hold great clinical potential,...
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Engineering plasmid copy number heterogeneity for dynamic microbial adaptation
Natural microbial populations exploit phenotypic heterogeneity for survival and adaptation. However, in engineering biology, limiting the sources of...
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CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples
Phylogenetic trees based on copy number profiles from multiple samples of a patient are helpful to understand cancer evolution. Here, we develop a...
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scGAL: unmask tumor clonal substructure by jointly analyzing independent single-cell copy number and scRNA-seq data
BackgroundAccurately deciphering clonal copy number substructure can provide insights into the evolutionary mechanism of cancer, and clustering...
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HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data
Bulk DNA sequencing of multiple samples from the same tumor is becoming common, yet most methods to infer copy-number aberrations (CNAs) from this...
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MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution
Aneuploidy, chromosomal instability, somatic copy-number alterations, and whole-genome doubling (WGD) play key roles in cancer evolution and provide...
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NestedBD: Bayesian inference of phylogenetic trees from single-cell copy number profiles under a birth-death model
Copy number aberrations (CNAs) are ubiquitous in many types of cancer. Inferring CNAs from cancer genomic data could help shed light on the...
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Accounting for 16S rRNA copy number prediction uncertainty and its implications in bacterial diversity analyses
16S rRNA gene copy number (16S GCN) varies among bacterial species and this variation introduces potential biases to microbial diversity analyses...
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Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc
Copy number alterations (CNAs) are among the most important genetic events in cancer, but their detection from sequencing data is challenging because...
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Genome-wide investigation to assess copy number variants in the Italian local chicken population
BackgroundCopy number variants (CNV) hold significant functional and evolutionary importance. Numerous ongoing CNV studies aim to elucidate the...
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Measurement of transgene copy number in transgenic tobacco plants producing human interferon-γ (hIFN-γ) using quantitative real-time PCR
In transgenic plants, the transgene copy numbers can highly affect the level of expression and genetic stability of the transgene. Hence, the first...
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ConDoR: tumor phylogeny inference with a copy-number constrained mutation loss model
A tumor contains a diverse collection of somatic mutations that reflect its past evolutionary history and that range in scale from single nucleotide...
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SCONCE2: jointly inferring single cell copy number profiles and tumor evolutionary distances
BackgroundSingle cell whole genome tumor sequencing can yield novel insights into the evolutionary history of somatic copy number alterations....
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Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes
Genome instability and aberrant alterations of transcriptional programs both play important roles in cancer. Single-cell RNA sequencing (scRNA-seq)...
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dbCNV: deleteriousness-based model to predict pathogenicity of copy number variations
BackgroundCopy number variation (CNV) is a type of structural variation, which is a gain or loss event with abnormal changes in copy number. Methods...
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Copy Number Variation and Expression Dynamics of the Dominant Vernalization-A1a Allele in Wheat
Adaptability of wheat to various environmental conditions, and wheat’s seasonal growth habits and the development rate are mainly controlled by...
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Evaluation of somatic copy number variation detection by NGS technologies and bioinformatics tools on a hyper-diploid cancer genome
BackgroundCopy number variation (CNV) is a key genetic characteristic for cancer diagnostics and can be used as a biomarker for the selection of...
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Identifying the driver miRNAs with somatic copy number alterations driving dysregulated ceRNA networks in cancers
BackgroundMicroRNAs (miRNAs) play critical roles in cancer initiation and progression, which were critical components to maintain the dynamic balance...
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Association between Sperm Mitochondrial DNA Copy Number and Concentrations of Urinary Cadmium and Selenium
Elevated sperm mitochondrial DNA copy number (mtDNAcn) is associated with damage to sperm and poorer measures of semen quality. Exposure to cadmium...
